In the year 2067, eight years after the events in Macross Frontier, a deadly new disease, the "Var Syndrome," threatens the galaxy. The Tactical Sound Unit, "Walküre," under the protection of the Valkyrie "Delta Flight," join together to combat this new threat. During a Var Syndrome outbreak, the Walkure unit is suddenly attacked by the mysterious "Aerial Knight" Valkyrie Team from the Kingdom of the Wind, the motivation for which remains a mystery...
At a concert on the nearby planet Randall, Freyja makes her official debut as the newest member of Walküre. The Aerial Knights of Windermere interrupt the festivities and finally make their true intentions known.
Mirage is assigned to train Hayate, who has become the newest recruit for Delta Flight. Freyja continues her Walküre training. As Hayate and Freyja both struggle through their respective initiations, they soon discover that they are stronger together than they are apart.
In the aftermath of the Var Syndrome Outbreak on Al Shahal, new opportunities present themselves for Freyja and Hayate. They make their way to Planet Ragna where Freyja auditions to be the newest member of Walkure, and Hayate receives an intriguing offer from Delta Flight.
Looking to escape the confines of an arranged marriage on her home planet, Freyja Wion stows away on a cargo ship, hoping to follow her dreams and audition for the Walkure Tactical Music Unit. She's discovered by Hayate Immelmann, a young dock worker and drifter with no particular dreams of his own. After an outbreak of the deadly Var Syndrome strikes, the Walkure Unit appears on the scene, and the power of Freyja's music is awakened.
At the Jellyfish Festival on Ragna, Messer says goodbye, as he reveals that he has been reassigned as a training instructor due to his worsening condition. Meanwhile, the Windermearans have developed a new system to amplify Prince Heinz' wind song. The Aerial Knights launch a surprise attack and Var Outbreak on Al-Shahal to test the new system. The Delta team must protect Al-Shahal from the Knights' attack even though they are one man short...
Hayate and Freyja continue to be put through their paces as the war with the Windermere Kingdom begins. Mikumo challenges Freyja to find what she's fighting for, while Messer gives harsh criticism to both Mirage and Hayate hoping to strengthen their resolve for the war to come. When the Aerial Knights attack, Hayate is put in an impossible situation and is forced to make a decision that will change his life forever.
Windermere's endgame is set into motion, as the ultimate plan for the Singer of the Stars is revealed. Xaos gets recalled to Ragna to prepare for the final showdown against Windermere.
While Mikumo and Hayate are both recovering from the infiltration on Voldor, Berger Stone from the Epsilon Group meets with Delta Flight and Walküre and reveals how the power of song and the Var Syndrome are related.
Hayate, Freyja, and Mirage have been captured by the Aerial Knights, and it's up to the rest of Walküre and Delta Flight to stage a daring rescue. Freyja and Hayate discover what happens when they are truly in sync. Meanwhile, Messer must deal with his worsening condition.
The Windermerans and the Sigur Berrentzs go on the offensive and launch an attack on NUNS forces. The Macross Elysion is ordered to leave its post on Ragna and to meet the Windermerean threat in space. Mirage receives surprising news from Major Arad about her status in Delta Flight.
Delta Flight and Walküre infiltrate Voldor once again, this time to test the Protoculture ruins' reaction to Walküre's live music. Freyja and Hayate encounter the enemy face to face, and are surprised at what they find. Mikumo tests her limits to potentially disastrous results.
Delta Flight and Walkure devise a plan to interrupt the Windermeran Mind Control in the Brisingr Cluster, using a special Walkure concert as a distraction. Hayate learns the shocking truth about his father.
Hayate and Freyja's fold resonance is put to the test. When both become discouraged, Mirage steps in to straighten things out. Keith begins to suspect Roid's true intentions. Makina, Reina and Kaname search for answers about Mikumo.
Walküre and Delta Flight infiltrate the planet Voldor, which has been occupied by the Aerial Knights of the Windermere Kingdom. The source behind the increased Var Syndrome Outbreaks is revealed.
Following the Windermere Kingdom's declaration of war on the New United Government, Delta Flight and Walküre are given new orders to defend Ragna from upcoming attacks. When rumors of Freyja being a Windermerian spy surface, she and Hayate take a joyride in his Siegfried unit to clear their heads.
Xaos goes on the offensive and pushes on with their plan to invade Windermere. Freyja and Hayate return to active duty, under special orders from Major Arad, leaving Mirage responsible for the two of them. Keith and Heinz clear the air. Cassim rides the wind.
Delta Flight and Walküre finally land on Windermere, on a mission to destroy the Protoculture system with a Tactical Live show. Their plans go awry when the Aerial Knights discover their presence and move to intercept them. Meanwhile, Roid has bigger things planned for Mikumo.
The extent of Messer's condition is finally revealed. The Aerial Knights make a move on Ragna while most of the Elysion squadrons are out on patrol, and a weakened Messer must fight through his illness to protect the others. Meanwhile, rumors begin to circulate about a blossoming romance between Hayate and Mirage.